Fast simulations of multidimensional NMR spectra of proteins and peptides

Thomas Vosegaard

doi:10.1002/mrc.4663

Fast simulations of multidimensional NMR spectra of proteins and peptides

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Abstract

To simulate full multidimensional nuclear magnetic resonance spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMulation Program for SOlid-state NMR (SIMPSON) to calculate total correlation spectroscopy transfer amplitudes and average distances as a source for nuclear Overhauser effect spectroscopy transfer amplitudes. Simulated ¹H 1D, 2D total correlation spectroscopy, and 2D nuclear Overhauser effect spectroscopy nuclear magnetic resonance spectra of peptides with sequence Pro─Ala─Gly─Tyr─Asn and Asn─Phe─Gly─Ala─Ile─Leu and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer.

Original language	English
Journal	Magnetic Resonance in Chemistry
Volume	56
Issue	6
Pages (from-to)	438-448
Number of pages	11
ISSN	0749-1581
DOIs	https://doi.org/10.1002/mrc.4663
Publication status	Published - Jun 2018

Keywords

NOESY
SIMPSON
TOCSY
chemical shift prediction
simulated spectra

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10.1002/mrc.4663Licence: CC BY-NC

Fast simulations of multidimensional NMR spectra of proteins and peptides 1Accepted manuscript, 2.25 MBLicence: Other
Vosegaard-2018-Magnetic_Resonance_in_ChemistryFinal published version, 683 KBLicence: CC BY-NC

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AB - To simulate full multidimensional nuclear magnetic resonance spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMulation Program for SOlid-state NMR (SIMPSON) to calculate total correlation spectroscopy transfer amplitudes and average distances as a source for nuclear Overhauser effect spectroscopy transfer amplitudes. Simulated 1H 1D, 2D total correlation spectroscopy, and 2D nuclear Overhauser effect spectroscopy nuclear magnetic resonance spectra of peptides with sequence Pro─Ala─Gly─Tyr─Asn and Asn─Phe─Gly─Ala─Ile─Leu and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer.

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KW - TOCSY

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Fast simulations of multidimensional NMR spectra of proteins and peptides

Abstract

Keywords

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